Abstract Separation and determination of water- and fat-soluble vitamins by micellar (MEKC) and microemulsion electrokinetic chromatography (MEEKC) are compared. MEKC is only useful in the quantitative analysis of water-soluble vitamins when sodium dodecylsulfate (SDS) is used as the surfactant. However, the separation of mixtures containing water- and fat-soluble vitamins is only achieved by MEEKC using a microemulsion prepared by mixing SDS as the surfactant, butanol as the co-surfactant, octane as the non-polar modifier and propanol as the second co-surfactant. The injection time and the solvent used for the dilution of samples have a significant effect on the analysis of lypophilic compounds. The most reproducible results in the analysis of fat-soluble vitamins are obtained by using the same microemulsion electrolyte as the solvent for samples and an injection time of 10 s.